Check 'IP Addresses' on the summary page of the appliance. Please note that Virtual Appliance does not come with vmware tools installed so IP Address would not be displayed until vmware tools are installed.

Amazon AWS:

use Public IP Addresses or Public DNS listed in your EC2 management console.

How can I enable emails for lost passwords, notes, and ontology processing?

Emails are sent via the ontologies_api project on the Appliance. You need to provide a valid mail server (smtp) configuration. The configuration should be provided in the /srv/ncbo/ontologies_api/current/config/environments/production.rb file.

Here are the available settings:

config.enable_notifications = true # Set to 'true' to send emails
config.email_sender = "admin@example.org" # Default sender for emails
config.email_disable_override = true # If this is set to 'false', all emails will be sent to the email configured in the 'email_override' setting
config.email_override = "admin@example.org"
config.smtp_host = "smtp.example.org"
config.smtp_port = 25
config.smtp_auth_type = :none # :none, :plain, :login, :cram_md5
config.smtp_user = "username" # only used if auth_type is not :none
config.smtp_password = "password" # only used if auth_type is not :none
config.smtp_domain = "example.org"

Once you have changed your settings, you will need to restart the server by running the command /sbin/service unicorn restart

Can I use the Annotator and Recommender on their own?

Because services like the Annotator and Recommender depend on the Ontologies API in BioPortal, you can not usefully install those services in a stand-alone way without also installing the core BioPortal software and ontologies.

Ontology Management

How do I add or change categories or groups?

There is currently no UI administrator interface (though this will likely be added in future versions). Categories and groups can be added using a console after logging into the Appliance as the ncbobp user.

This will prevent the “Downloads” column in the Submissions table from appearing on ontology summary pages.

If you want to restrict download via the REST endpoint, you need to modify your environment configuration files (e.g., production.rb, staging.rb, etc.) in your ontologies_api project. The production.rb file should contain a “config.restrict_download” property -- there’s an example of what it should look like in the sample configuration file in GitHub:

Ontology Parsing

When are new ontologies parsed?

The ncbo_cron project uses a scheduler to run a process that collects new ontology submissions and parses them, adds them to the search index, calculates metrics, and processes them for use with the annotator. You can also parse ontologies manually.

How do I manually parse an ontology?

To manually parse an ontology, you will need to interact with the code using the console after switching to ncbobp user:

How can I process a UMLS ontology?

UMLS ontologies can be processed to work with our system by converting them to RDF. There is no automated way to do this and you must have your own UMLS MySQL installation and a OSX/Linux/Unix machine with 8GB+ of RAM in order for the conversion process to work. The scripts to convert UMLS to RDF are available on Github.

Once you have converted UMLS to RDF, you will get Turtle (.ttl) files that can be uploaded using the BioPortal Web UI. Please select UMLS as the format for these ontologies.

How do I know if an ontology has parsed?

The BioPortal Web UI will cache information about ontologies for 60 seconds. After parsing is complete, just refresh the ontology summary page to see the status for the most recent submission listed under the "Submissions" table.

In addition, you can look at the REST service directly, which will always give you the most updated information. To do this, visit the following URL: